Clustering From Reduced Group Matrix

A K-medoids clustering of a group of subjects. Depending on the chosen method it produces a mean clustering (averaged) or a clustering for each subject of the group (concatenated).

Description

Usage example

regions_nomenclature:            /my/path/share/brainvisa-share-4.6/nomenclature/translation/nomenclature_desikan_freesurfer.txt

method:                          averaged approach

region:                          lh.inferiorparietal

subjects_group:                  /my/path/brainvisa_db/subjects/group_analysis/g1/g1_group.xml

intersubject_reduced_matrces:    '/my/path/brainvisa_dbsubjects/group_analysis/g1/connectivity_clustering/avg/studyA/lh.inferiorparietal/smooth3.0
                                 /g1_avg_studyA_lh.inferiorparietal_001_reduced_matrix_20to500mm.nii.gz'

average_mesh:                    /my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/averagebrain.white.gii

regions_parcellation:            '/my/path/freesurfer_db/group_analysis/average_mesh_group/average_brain/bh.annot.averagebrain.gii'

nb_clusters:                     12  

reduced_group_matrix:            /my/path/brainvisa_db/subjects/group_analysis/g1/connectivity_clustering/avg/studyA/lh.inferiorparietal/smooth3.0
                                 /g1_avg_studyA_lh.inferiorparietal_group_reduced_matrix_20to500mm.ima

ROI_clustering:                  '/my/path/brainvisa_db/subjects/group_analysis/g1/connectivity_clustering/avg/studyA/lh.inferiorparietal/smooth3.0
                                 /g1_avg_studyA_lh.inferiorparietal_avgSubject_clustering_20to500mm.gii'

Parameters

regions_nomenclature: Nomenclature ROIs File ( input )

Nomenclature of the cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas

method: Choice ( input )

Two methods are proposed:
(1) averaged approach to obtain an average result on the group.
(2) concatenated approach to obtain individual results across the group.

region: String ( input )

The study region based on regions_nomenclature file.

subjects_group: Group definition ( input )

The XML file corresponding to the subjects group.

intersubject_reduced_matrices: ListOf( Connectivity Matrix ) ( input )

Each subject obtains a reduced matrix from its individual complete matrix. There are as many reduced matrices as input subjects.

average_mesh: White Mesh ( input )

Freesurfer average white mesh of a group of subjects.

regions_parcellation: ListOf( ROI Texture ) ( input )

Cortical parcellation used to partition the study.
Example : Freesurfer Desikan_Killiany Atlas (?h.aparc.annot).

Implications of the choice of the method on the regions_parcellation parameter:
(1) averaged approach: the regions_parcellation parameter must be a file representing the average parcellation of the group of subjects.
(2) concatenated approach: the regions_parcellation parameter must be a list of files, each representing the individual parcellation of a subject of the group.

nb_clusters: Integer ( input )

Maximal number of clusters used to parcellate the study region.
Default to 12.

reduced_group_matrix: Connectivity Matrix ( output )

Group matrix dependant of the chosen method:
(1) averaged approach: a mean matrix of the reduced matrices of the group subjects.
(2) concatenated approach: a concatenation of the reduced matrices of the group subjects.

ROI_clustering: ListOf( Connectivity ROI Texture ) ( output )

A K-medoids clustering of the reduced_group_matrix.

Technical information

Toolbox : Constellation

User level : 2

Identifier : constel_group_clustering

File name : brainvisa/toolboxes/constellation/processes/group_pipeline/tools/constel_group_clustering.py

Supported file formats :

regions_nomenclature :

Text file, Text file

subjects_group :

XML, XML

intersubject_reduced_matrices :

gz compressed NIFTI-1 image, GIS image, NIFTI-1 image, gz compressed NIFTI-1 image

average_mesh :

GIFTI file, GIFTI file, MESH mesh, MNI OBJ mesh, PLY mesh, TRI mesh, Z compressed GIFTI file, Z compressed GIFTI file, Z compressed MESH mesh, Z compressed MNI OBJ mesh, Z compressed PLY mesh, Z compressed TRI mesh, gz compressed GIFTI file, gz compressed GIFTI file, gz compressed MESH mesh, gz compressed MNI OBJ mesh, gz compressed PLY mesh, gz compressed TRI mesh

regions_parcellation :

GIFTI file, GIFTI file, Texture

reduced_group_matrix :

GIS image, GIS image

ROI_clustering :

GIFTI file, GIFTI file, Texture